PCA plot module

Module UI + server to generate a pca plot.

Usage

pcaPlotUI(id, panel)

pcaPlotServer(id, obj, coldata, config)

Arguments

id

Module id

panel

string, can be 'sidebar' or 'main'

obj

reactiveValues object containing carnation object

coldata

reactiveValues object containing object metadata

config

reactive list with config settings

Value

UI returns tagList with PCA plot UI. Server invisibly returns NULL (used for side effects).

Examples

if (FALSE) { # interactive()
library(shiny)
library(DESeq2)

# Create reactive values to simulate app state
oobj <- make_example_carnation_object()

obj <- reactiveValues(
   dds = oobj$dds,
   rld = oobj$rld,
   res = oobj$res,
   all_dds = oobj$all_dds,
   all_rld = oobj$all_rld,
   dds_mapping = oobj$dds_mapping
)

# Set up coldata structure that the module expects
coldata <- reactiveValues(
  curr = list(
    all_samples = colData(oobj$dds$main),
    main = colData(oobj$dds$main)
  )
)

config <- reactiveVal(get_config())

shinyApp(
  ui = fluidPage(
         sidebarPanel(pcaPlotUI('p', 'sidebar')),
         mainPanel(pcaPlotUI('p', 'main'))
       ),
  server = function(input, output, session){
             pcaPlotServer('p', obj, coldata, config)
           }
)
}